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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Protein ligand interaction database (PLID).

A Srinivas Reddy1, H S Durga Amarnath, Raju S Bapi

  • 1Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad 500 007, Andhra Pradesh, India.

Computational Biology and Chemistry
|June 3, 2008
PubMed
Summary
This summary is machine-generated.

A new database, the protein ligand interaction database (PLID), offers extensive data on 6295 protein-ligand interactions. It details physico-chemical properties, quantum mechanical descriptors, and active site residues for enhanced drug discovery research.

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Last Updated: Jul 4, 2026

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Published on: April 3, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Understanding protein-ligand interactions is crucial for drug discovery and molecular biology.
  • Existing databases may lack comprehensive physico-chemical and quantum mechanical data for these interactions.

Purpose of the Study:

  • To create a comprehensive database of protein-ligand interactions.
  • To provide detailed physico-chemical properties, quantum mechanical descriptors, and active site residue information.

Main Methods:

  • Extraction of 6295 protein-ligand complexes from the Protein Data Bank (PDB).
  • Compilation of physico-chemical properties, quantum mechanical descriptors, and active site residue data.
  • Development of a publicly accessible web-based database (PLID).

Main Results:

  • The Protein Ligand Interaction Database (PLID) is established, containing 6295 ligands bound to proteins.
  • PLID offers the most comprehensive collection of physico-chemical properties, quantum mechanical descriptors, and active site residues currently available.
  • The database is accessible online at http://203.199.182.73/gnsmmg/databases/plid/.

Conclusions:

  • The PLID database serves as a valuable resource for researchers studying protein-ligand interactions.
  • Its comprehensive data facilitates advancements in drug design and molecular modeling.
  • Public accessibility promotes wider use and collaborative research in the field.